In an effort to identify genes in the substantia nigra which are relevant to neurodegeneration in Parkinson's disease (PD), we undertook a study utilizing laser capture microdissection and the micropunch techniques. RT-PCR and differential display were performed with the total RNA isolated from microdissected human brain substantia nigra compacta (SNC), ventral tegmental area (VTA) and laser captured mouse embryo substantia nigra neuroepithelial cells. Differentially expressed bands were identified by sequencing. Comparison of the embryonic substantia nigra neuroepithelium with a control region without dopamine cells (tectum) revealed a differential expression of a CAG repeat cDNA. The expression of a guanine nucleotide exchange factor (GEF) was found to be increased in the SNC of the PD brain compared to an age matched control. Also, NADH Ubiquinone oxidoreductase and cytochrome c oxidase (Complex I and Complex IV) whose functions are known to be altered in PD, along with twelve unknown cDNAs were found to be differentially expressed in the VTA of normal and PD brain. Catalase expression was increased, while that of Cox 2, hevin precursor protein and dynein were decreased in PD brains. In situ hybridization using riboprobes revealed one of the differentially expressed unknown cDNA obtained from human VTA to be expressed in a variety of interesting discrete regions and nuclei subpopulations. Similar in situ hybridization results were obtained with a riboprobe that has 78% homology to neurofilament protein. Unknown cDNAs will be identified by screening brain cDNA libraries. The differentially expressed cDNAs are being characterized using a variety of molecular biological techniques. Our future interests are to laser capture and microdissect discrete areas of the mouse embryo/adult brains and human postmortem brains in order to establish a cDNA expression pattern in a variety of neuro-degenerative diseases (e.g. Parkinson's, bipolar, schizophrenia).